if (!require(devtools)) install.packages("devtools")
## Loading required package: devtools
## Loading required package: usethis
devtools::install_github("yanlinlin82/ggvenn")
## Skipping install of 'ggvenn' from a github remote, the SHA1 (335cfe1e) has not changed since last install.
## Use `force = TRUE` to force installation
GeneSet Analysis
library(ggvenn)
## Loading required package: dplyr
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
## Loading required package: grid
## Loading required package: ggplot2
Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/GeneSets/Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/GeneSets/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/GeneSets/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
for (i in 1:9) {
Kahraman = read.csv(Kahraman_paths[i], header = FALSE)
Clemente = read.csv(Clemente_paths[i], header = FALSE)
Vitting = read.csv(Vitting_paths[i], header = FALSE)
Genelist <- list(
Kahraman_Study = Kahraman$V1,
Clemente_Study = Clemente$V1,
Vitting_Study = Vitting$V1
)
print(ggvenn(
Genelist,
fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
))
print(intersect(intersect(Kahraman, Clemente), Vitting))
}
## V1
## 1 TNC
## 2 ATXN3
## 3 FAM76B
## 4 CAP2
## 5 PNPLA7
## 6 PPAN
## 7 DACH1
## 8 CPLX1
## 9 SKA2
## 10 BICD2
## 11 HOXC6
## V1
## 1 C19orf60
## 2 OSBPL5
## 3 CD44
## 4 ZFYVE16
## 5 TLE2
## 6 ST6GALNAC1
## 7 LIMS2
## 8 CALD1
## 9 PNKD
## 10 SHC2
## 11 RIN2
## 12 MYO10
## 13 C7orf50
## 14 AK3
## 15 RABGEF1
## 16 TSPAN7
## 17 FMNL3
## 18 ING2
## 19 PCCA
## 20 SH3BGR
## 21 BTN3A2
## V1
## 1 CD44
## 2 RC3H2
## 3 CEACAM1
## 4 NRCAM
## 5 CDADC1
## 6 GSPT1
## 7 CAV1
## 8 DNMBP
## 9 LIPA
## 10 NCOA7
## 11 KTN1
## 12 PDGFRA
## 13 BCAR3
## 14 RGS3
## 15 TARS2
## 16 ZNF385B
## 17 OBSCN
## 18 NAGS
## 19 BSCL2
## 20 PCMTD1
## 21 AP1S2
## 22 EXD3
## 23 ZNF44
## 24 WWP2
## 25 CTNND1
## 26 SCAMP5
## V1
## 1 KIF22
## 2 NXT2
## 3 NT5E
## 4 GBAS
## 5 PANK1
## 6 CXADR
## 7 MFAP4
## 8 NUDT6
## 9 FGGY
## 10 AQP1
## V1
## 1 SPAG9
## 2 LSR
## 3 ITM2C
## 4 CXADR
## 5 CPLX1
## 6 TNFRSF10C
## V1
## 1 CASP10
## 2 SDCCAG8
## 3 ATXN3
## 4 CECR1
## 5 DYRK1B
## 6 LSR
## 7 MEST
## 8 GAB1
## 9 CNOT2
## 10 MKLN1
## 11 SHROOM2
## 12 NTRK2
## 13 DST
## 14 IL17RE
## 15 PPFIBP2
## 16 WWOX
## 17 CTNND1
## V1
## 1 VAMP1
## V1
## 1 CFH
## 2 C1orf198
## 3 FAM174B
## V1
## 1 PLEKHH1
## 2 FGFR2
## 3 BAZ2A
## 4 SMARCA2
## 5 IPO11
## 6 CECR1
## 7 PATZ1
## 8 ASB9
## 9 FLT1
## 10 DOCK8
## 11 DNMBP
## 12 SHOC2
## 13 MVK
## 14 MXI1
## 15 ACOT9
## 16 PSD4
## 17 EPS8L1
## 18 PDGFRA
## 19 BIVM
## 20 CIB2
## 21 BIN1
## 22 BCAR3
## 23 NCOA4
## 24 RNF185
## 25 DCDC2
## 26 ZNF185
## 27 TM7SF2
## 28 SCOC
## 29 CXADR
## 30 RABGEF1
## 31 SLC35B2
## 32 KALRN
## 33 GOLGA8A
## 34 GRAMD1C
## 35 LIMK2
## 36 AFMID
## 37 RBM33
## 38 WWP2
## 39 SCAMP5
Isoform Switch Analysis
Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
for (i in 1:9) {
Kahraman = read.csv(Kahraman_paths[i], header = TRUE)
Clemente = read.csv(Clemente_paths[i], header = TRUE)
Vitting = read.csv(Vitting_paths[i], header = TRUE)
Genelist <- list(
Kahraman_Study = Kahraman$Normal_Isoform_Cancer_Isoform,
Clemente_Study = Clemente$Normal_Isoform_Cancer_Isoform,
Vitting_Study = Vitting$Normal_Isoform_Cancer_Isoform
)
print(ggvenn(
Genelist,
fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
))
print(intersect(intersect(Kahraman, Clemente), Vitting))
}
## Normal_Isoform_Cancer_Isoform
## 1 uc003gbj_uc003gbi
## 2 uc004aso_uc004asp
## 3 uc003ncb_uc011djb
## Normal_Isoform_Cancer_Isoform
## 1 uc002vhm_uc002vhq
## Normal_Isoform_Cancer_Isoform
## 1 uc002otv_uc002otw
## 2 uc001mvx_uc001mvw
## 3 uc002unj_uc002unn
## Normal_Isoform_Cancer_Isoform
## 1 uc003iew_uc003iex
## 2 uc003tbv_uc010kwf
## 3 uc003pko_uc010kbr
## 4 uc003tre_uc003trf
## 5 uc002yki_uc002ykj
## 6 uc001kgn_uc001kgo
## 7 uc001qyu_uc001qyt
## Normal_Isoform_Cancer_Isoform
## 1 uc003gbj_uc003gbi
## 2 uc002yki_uc002ykj
## Normal_Isoform_Cancer_Isoform
## 1 uc002uxj_uc010ftb
## 2 uc002nym_uc002nyn
## 3 uc003vqg_uc003vqc
## [1] Normal_Isoform_Cancer_Isoform
## <0 rows> (or 0-length row.names)
## [1] Normal_Isoform_Cancer_Isoform
## <0 rows> (or 0-length row.names)
## Normal_Isoform_Cancer_Isoform
## 1 uc001kza_uc001kyy
## 2 uc003akb_uc003ake
## 3 uc002bdb_uc002bdc
## 4 uc002yki_uc002ykj
## 5 uc003aks_uc003akr
## 6 uc003eas_uc003eaq
Normal Isoform Analysis
library(tidyr)
Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch//Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
for (i in 1:9) {
Kahraman = read.csv(Kahraman_paths[i], header = TRUE)
Kahraman_Normals <- (Kahraman %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"), "_"))[,1][2:length(Kahraman[,1])]
Clemente = read.csv(Clemente_paths[i], header = TRUE)
Clemente_Normals <- (Clemente %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"), "_"))[,1][2:length(Clemente[,1])]
Vitting = read.csv(Vitting_paths[i], header = TRUE)
Vitting_Normals <- (Vitting %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"), "_"))[,1][2:length(Vitting[,1])]
Genelist <- list(
Kahraman_Study = unique(Kahraman_Normals),
Clemente_Study = unique(Clemente_Normals),
Vitting_Study = unique(Vitting_Normals)
)
print(ggvenn(
Genelist,
fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
))
print(intersect(intersect(Kahraman_Normals, Clemente_Normals), Vitting_Normals))
}
## [1] "uc003gbj" "uc004aso" "uc003ncb" "uc001sev"
## [1] "uc002tpa" "uc001voo" "uc001lxk" "uc002njv" "uc002vhm" "uc002jsh"
## [7] "uc003kgq" "uc002loq" "uc003jft" "uc003ziq" "uc004deg" "uc002yya"
## [1] "uc002otv" "uc001qba" "uc004cxi" "uc004cmp" "uc001mvx" "uc001nup"
## [7] "uc003vfc" "uc003han" "uc002unj" "uc002ies"
## [1] "uc003iew" "uc003tbv" "uc002gvt" "uc003pko" "uc003tre" "uc002yki"
## [7] "uc001kgn" "uc003hzc" "uc001qyu" "uc004eof"
## [1] "uc002vqz" "uc003gbj" "uc003xcy" "uc002yki"
## [1] "uc002uxj" "uc002nym" "uc002ffk" "uc004csu" "uc011chq" "uc009zro" "uc003vqg"
## [8] "uc003btw"
## character(0)
## [1] "uc001hub" "uc010boe"
## [1] "uc001kzl" "uc009zvk" "uc001kza" "uc001vps" "uc002tob" "uc003akb"
## [7] "uc001oct" "uc003oxd" "uc003vcm" "uc002zmj" "uc002bdb" "uc002yki"
## [13] "uc001xjl" "uc003han" "uc011che" "uc002jva" "uc003aks" "uc004cwk"
## [19] "uc004dap" "uc002tjc" "uc002qis" "uc003ndx" "uc003eas"
Cancer Isoform Analysis
library(tidyr)
Kahraman_paths <- file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch//Kahraman", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Clemente_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Clemente", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
Vitting_paths = file.path("/Users/tulaykarakulak/Documents/PhD/Review/Data_Comparison/ForRVenn/IsoSwitch/Vitting/", c("BRCA_cancer","COAD_cancer","KICH_cancer","LIHC_cancer","LUAD_cancer","LUSC_cancer","PRAD_cancer","THCA_cancer","KIRC_cancer"))
for (i in 1:9) {
Kahraman = read.csv(Kahraman_paths[i], header = TRUE)
Kahraman_Cancer <- (Kahraman %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"), "_"))[,2][2:length(Kahraman[,1])]
Clemente = read.csv(Clemente_paths[i], header = TRUE)
Clemente_Cancer <- (Clemente %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"), "_"))[,2][2:length(Clemente[,1])]
Vitting = read.csv(Vitting_paths[i], header = TRUE)
Vitting_Cancer <- (Vitting %>% separate(Normal_Isoform_Cancer_Isoform, c("Normal", "Cancer"), "_"))[,2][2:length(Vitting[,1])]
Genelist <- list(
Kahraman_Study = unique(Kahraman_Cancer),
Clemente_Study = unique(Clemente_Cancer),
Vitting_Study = unique(Vitting_Cancer)
)
print(ggvenn(
Genelist,
fill_color = c("skyblue1", "#EFC000FF", "tomato1"),
stroke_size = 0.3, set_name_size = 4,text_color = "black", text_size = 2
))
print(intersect(intersect(Kahraman_Cancer, Clemente_Cancer), Vitting_Cancer))
}
## [1] "uc003gbi" "uc004asp" "uc002uhz" "uc011djb"
## [1] "uc003sju" "uc003tvh" "uc002uhz" "uc002vhq" "uc009xkg"
## [1] "uc002otw" "uc003qai" "uc001mvw" "uc001dpy" "uc002unn"
## [1] "uc003iex" "uc010kwf" "uc010kbr" "uc003trf" "uc002ykj" "uc001kgo" "uc001qyt"
## [8] "uc002dts"
## [1] "uc003gbi" "uc002ykj"
## [1] "uc010ftb" "uc002nyn" "uc003pdc" "uc003vqc"
## character(0)
## [1] "uc009xkg"
## [1] "uc001kyy" "uc003ake" "uc003tvh" "uc003ehk" "uc002bdc" "uc001dpy" "uc002ykj"
## [8] "uc003akr" "uc003eaq"